bioregistry 0.13.10__py3-none-any.whl → 0.13.12__py3-none-any.whl

bioregistry/validate/cli.py

@@ -102,3 +102,19 @@ def validate_virtuoso(
         url, strict=not relax, use_preferred=use_preferred, context=context
     )
     click_write_messages(messages, tablefmt=tablefmt)
+
+
+@validate.command(name="linkml")
+@click.argument("url")
+@RELAX_OPTION
+@CONTEXT_OPTION
+@PREFERRED_OPTION
+@FORMAT_OPTION
+def validate_linkml(
+    url: str, relax: bool, use_preferred: bool, context: str | None, tablefmt: str | None
+) -> None:
+    """Validate prefixes in a LinkMK YAML configuration."""
+    from .utils import click_write_messages, validate_linkml
+
+    messages = validate_linkml(url, strict=not relax, use_preferred=use_preferred, context=context)
+    click_write_messages(messages, tablefmt=tablefmt)

bioregistry/validate/utils.py

@@ -5,7 +5,7 @@ from __future__ import annotations
 import json
 from collections.abc import Callable, Mapping
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Literal
+from typing import TYPE_CHECKING, Any, Literal, cast
 
 import click
 from pydantic import BaseModel
@@ -18,6 +18,7 @@ __all__ = [
     "Message",
     "click_write_messages",
     "validate_jsonld",
+    "validate_linkml",
     "validate_ttl",
     "validate_virtuoso",
 ]
@@ -150,6 +151,13 @@ def validate_virtuoso(url: str, **kwargs: Any) -> list[Message]:
     return _get_all_messages(inputs, **kwargs)
 
 
+def validate_linkml(url: str, **kwargs: Any) -> list[Message]:
+    """Validate a LinkML YAML configuration's prefix map."""
+    prefix_map = get_linkml_prefix_map(url)
+    inputs: list[tuple[str, str, int | None]] = [(k, v, None) for k, v in prefix_map.items()]
+    return _get_all_messages(inputs, **kwargs)
+
+
 def _get_all_messages(
     inputs: list[tuple[str, str, int | None]],
     *,
@@ -309,3 +317,22 @@ def get_virtuoso_prefix_map(url: str) -> dict[str, str]:
         )
     rv = {left.text: right.text for left, right in table_body_tag.find_all("tr")}
     return rv
+
+
+def get_linkml_prefix_map(url: str) -> dict[str, str]:
+    """Get the prefix map from a LinkML YAML configuration.
+
+    :param url: The URL for the LinkML YAML configuration. Examples:
+
+        - https://github.com/HendrikBorgelt/CatCore/raw/refs/heads/main/src/catcore/schema/catcore.yaml
+        - https://github.com/mapping-commons/sssom/raw/refs/heads/master/src/sssom_schema/schema/sssom_schema.yaml
+
+    :returns: The prefix map defined in the LinkML configuration
+    """
+    import requests
+    import yaml
+
+    res = requests.get(url, timeout=5)
+    res.raise_for_status()
+    data = yaml.safe_load(res.text)
+    return cast(dict[str, str], data["prefixes"])

bioregistry/version.py

@@ -11,7 +11,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.13.10"
+VERSION = "0.13.12"
 
 
 def get_git_hash() -> str | None:

{bioregistry-0.13.10.dist-info → bioregistry-0.13.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioregistry
-Version: 0.13.10
+Version: 0.13.12
 Summary: Integrated registry of biological databases and nomenclatures
 Keywords: snekpack,cookiecutter,databases,biological databases,biomedical databases,persistent identifiers
 Author: Charles Tapley Hoyt

{bioregistry-0.13.10.dist-info → bioregistry-0.13.12.dist-info}/RECORD

@@ -1,5 +1,5 @@
 bioregistry/.DS_Store,sha256=MtEQz-j0qLB8mBzZ2s0qvjaV6xHF3Z2A1YUEa_dogB8,10244
-bioregistry/__init__.py,sha256=ghFOK7i2zfm5vEwVF-xXuivIMD7giyImmmbhHlMfEQo,6742
+bioregistry/__init__.py,sha256=LZF2oEQZoKh4DC38reMoH31dNJR7kQO8dwqpMv5NVqw,6780
 bioregistry/__main__.py,sha256=hfyt3xyxKdAp969VpjqhTMdpG7CxtDCA7y8bYc0-ZKU,92
 bioregistry/analysis/__init__.py,sha256=z0F0QjavayAY0-otbu92g1wR3KK5ZmRNS24r76nxVJI,41
 bioregistry/analysis/bioregistry_diff.py,sha256=0GEjk3OgjToUKO0nH4RmFUpZl8L2rikSy0qDDtqB2o4,10278
@@ -21,8 +21,8 @@ bioregistry/app/static/nfdi4chem.svg,sha256=jjHtKDadcnfgkfU_NGpuXb8E4oH8stbyWftZ
 bioregistry/app/static/northeastern.svg,sha256=1TOrV0kNHLM9iEMhXjZBt1WYwmSRHmyJ5wSkNpfckdE,7086
 bioregistry/app/static/rwth-iac.svg,sha256=UpvCVjb9wflykVH-8r1QkpI5zEz-ID72nnobFQv6nP4,19228
 bioregistry/app/templates/.DS_Store,sha256=-h9BoY3FbmzzXlHeJRERn_I7ipCKSoYZbNch6jKcGHM,6148
-bioregistry/app/templates/base.html,sha256=BQxzPOOzuTu3Z-y4pio5nZGZNExpoUxqxJgmwQfW4Jc,10799
-bioregistry/app/templates/collection.html,sha256=Tgd4lkCNl2Bguw5wgq1yMj1kwv81V3fpwH_lsSx74GU,3761
+bioregistry/app/templates/base.html,sha256=6QXePUhDYMIIaDYxVdsvricVyj7itmXSkTOsh0BpDF4,10967
+bioregistry/app/templates/collection.html,sha256=JGsfojujafDhFJKJh7hrUnKwo2w6rkppQOBkxwI0GmY,4135
 bioregistry/app/templates/collections.html,sha256=3G7qtao8nPlbMJN2i9DjwGvTqLi0Rbvl9_Vl7W48RPc,3474
 bioregistry/app/templates/context.html,sha256=LptXmIMJiQEeZXYaC4KEQq6CnZGvbj6KI_Nub6I800k,6754
 bioregistry/app/templates/contexts.html,sha256=tYJpX6i58mIfA-QdUKg_cXAK6zuReR1ZmSyMpkdlmhw,2379
@@ -50,7 +50,9 @@ bioregistry/app/templates/resolve_errors/disallowed_identifier.html,sha256=jWQA0
 bioregistry/app/templates/resolve_errors/invalid_identifier.html,sha256=l0A8r1xhjSoqyfj5YagWnEbUaZgxYKKZN5VzSLFbIYc,2064
 bioregistry/app/templates/resolve_errors/missing_prefix.html,sha256=1c2lqB5bd2NycaAaV9bFKi23TUTncG8ywNReDxGTAS4,1568
 bioregistry/app/templates/resolve_errors/missing_providers.html,sha256=9xFAcxM7ooGbipOB48sGbSwjD9t892L9RnceMd6QuwI,1339
-bioregistry/app/templates/resource.html,sha256=5heriFhs2yaLAehxsYaRBmHA5Q6KUkzQSHr5DqhX1sI,41303
+bioregistry/app/templates/resource-bibliometrics.html,sha256=mb5q3M-RpOK6_PSkfUyGroHDdHUuBY1qKEqJdxLnDjs,3451
+bioregistry/app/templates/resource-standards.html,sha256=lI8MYT04Ob9UdZ1bqegrg7BYpysertk83tbEpShfyD8,4330
+bioregistry/app/templates/resource.html,sha256=aReg1no9h8DGXzfNCV11CuHyILuhkP74agPP2IPDaaI,32133
 bioregistry/app/templates/resources.html,sha256=HJdvJtF2FrkEVyfGLKD_5G0wlqDXEJrxzdJwObzLxTA,3930
 bioregistry/app/test.py,sha256=mr0erF32i45CWbkdoJeb907FTKoYiJsjUIe-XA_G2qI,2057
 bioregistry/app/ui.py,sha256=Fh2Aq2q6ZJRQhLlbgnZ7xTzqMQFGxXKIqpb2Tu_0uzo,23934
@@ -74,6 +76,8 @@ bioregistry/curation/add_co_providers.py,sha256=s14caK1lCRLBEW_NsbgIV93eqoBpr56k
 bioregistry/curation/add_descriptions_from_gs.py,sha256=v5qomc7NSdPiSHOJZAsf7Jsc7Ia7Pcz7xu0e7Ejso6M,1055
 bioregistry/curation/add_examples.py,sha256=3S2F4BrbJebWG32AvnBG4rb0rzTC2mBuZzVucx58YcA,1295
 bioregistry/curation/add_examples_from_ols.py,sha256=g09hNkni-4jR_hzaJ-IYN8J8TV2Jk91htwXPDwi85As,2961
+bioregistry/curation/add_linkml.py,sha256=mOAFlovm6RgQwAozOCNF0JjduKMx_IMa2N797pN4GJ4,2475
+bioregistry/curation/add_nfdi_section_collections.py,sha256=n6zpSSTTj_16FKLZSKm4ws3nPL7nvHag3S5FPRBu1wI,2034
 bioregistry/curation/add_ontology_regexes.py,sha256=QdsMrma7meYPK_xCLj8U13XPM6ayWPG_LyL3WiAe7y4,1624
 bioregistry/curation/add_provider_status_curations.py,sha256=_ydRS1AT4z06z1Ur9If7eyuSmWRoCMZQGM9t2dpofdI,1956
 bioregistry/curation/add_sweet.py,sha256=ooVbCzzoicj1Q0xsYCYF4CSt4GKLQUCMSy-lfiCue2E,5060
@@ -103,11 +107,11 @@ bioregistry/curation/suggest_author_curation.py,sha256=ecD9v6yOx5LbTAi0_wNhk9fKO
 bioregistry/curation/suggest_uniprot_providers.py,sha256=b9_LZ9hjavJ0iigGThZJuH_wEjVWCu3njJWdwvBSXj4,835
 bioregistry/data/README.md,sha256=vlWWGV0jOmcm4wu1hGUq01jZa41rDwfqIDffVs2somg,1796
 bioregistry/data/__init__.py,sha256=6oMVGRsmEoVd5caRr1Q_Zk-u3rOj382rIi2AoGMEVc8,41
-bioregistry/data/bioregistry.json,sha256=0ZWnbXyIhlakf8peL-H4XN1PbjIbrDhYZiU_LfvwZWg,6380512
-bioregistry/data/collections.json,sha256=A5lqwOekyQwfT2SK81GoxCk0XS5s-cDb_qw7M43JfrA,32633
+bioregistry/data/bioregistry.json,sha256=gcF4zU1srSRGDyUlhC25WF15thyw2S1ul3r4bulCBAE,6393747
+bioregistry/data/collections.json,sha256=m05boqYauMGm2rYLBITMRygYHU9EY0TlCDNCwaT-4W8,45771
 bioregistry/data/contexts.json,sha256=nUHDGrZe2oF9P5I8CeMoEYsaUfwNweTc5n7t8Hj2iJw,1436
 bioregistry/data/curated_mappings.sssom.tsv,sha256=n5l_fOSDmzV23gUQhgnefdqqJGyLwyH7YE9FGGIn3Gc,45034
-bioregistry/data/curated_papers.tsv,sha256=XdqIGcP1s2xbIn9851M_3wjOnNbIqTlvGeJqbg2rlVo,27397
+bioregistry/data/curated_papers.tsv,sha256=Ldb0f42mu6gYWbe6bwLSo0xurQ9NE3MXW3PqJrmb1BU,27481
 bioregistry/data/metaregistry.json,sha256=Icu0SHyyTHfHRkCne5itdjPy-1fNAk72Gf09o-fBryA,63800
 bioregistry/export/__init__.py,sha256=EfApHN9voMJt4sr3T-U6r50szl7I3QBnaw0s7KKjkek,35
 bioregistry/export/__main__.py,sha256=u9XDrUWAC952AzgUNHlfFPhDl0tBPVv_PChPRxKJhOY,96
@@ -124,18 +128,18 @@ bioregistry/export/yaml_export.py,sha256=08W93quZWirWv5TltvgltKxWbF1nMlzrlWsVocc
 bioregistry/external/.DS_Store,sha256=Z9kAJuxxll_hDHDy-OWxUT4EEDpbh4KAuaMfi5CYz7s,14340
 bioregistry/external/__init__.py,sha256=cjcfwBprqBx_X8IJh6Vug6gGgbCf5vLcJAe4Ql_0Cuc,2989
 bioregistry/external/aberowl/__init__.py,sha256=5xOVxU7SMXlTvI0zWi6cMbiga1jVXD0Joh-N_rBH1As,2475
-bioregistry/external/aberowl/processed.json,sha256=7dk3dP6s23SAT6rzYOzdkdWzHjsHkYRQ9yyxcU5dg3k,746926
+bioregistry/external/aberowl/processed.json,sha256=eveGQAZB_38rPZZIFKZ6vyDNyjUDxJmvsCf_S0IvKGg,751341
 bioregistry/external/align.py,sha256=x2N910eaTHFR5BnvwuWRC9Me2z2PsKPaBeK78inoujU,2101
 bioregistry/external/alignment_utils.py,sha256=CcSFc6bMiyTiLsASKsSVpaEBoK5UC36xIffTdzcLvw8,11752
 bioregistry/external/bartoc/__init__.py,sha256=lbtUoxCLyWFIMkmIxPA7TTmbgoDEQTfd0GQcclBtEcU,3173
-bioregistry/external/bartoc/processed.json,sha256=bqkBdFtSHHPOsCNcCCoggRx-NzCiNssg8laTdNYZBb4,2536923
+bioregistry/external/bartoc/processed.json,sha256=AUkcvliNg_vCt-e4q5EOB0TfOI5gPDxT9iaTuMJ7s5k,2547094
 bioregistry/external/biocontext/__init__.py,sha256=gLytdKfeN2dFIW_ugl4W5hJetfciMs171uzeMiHMCdo,2589
 bioregistry/external/biocontext/processed.json,sha256=XRUGK63S5OVRBS0BrbUjepsFI8NPVVVZFmeWbbfXWUQ,74913
 bioregistry/external/biolink/__init__.py,sha256=o57Dhg5Z65oYYe-RU0S6q0OKjc8p-uTk3s3iqroAUXM,2613
 bioregistry/external/biolink/processed.json,sha256=vGT0La8q9dJ1TTwRM9ZNmT7HRPCFdVqA_oQPpoT2LeI,10725
 bioregistry/external/biolink/processing_biolink.json,sha256=lITU-JFBbXU0FEQR3q1Y9A8E_2YxRHyHnzogqadGKtI,508
 bioregistry/external/bioportal/__init__.py,sha256=zXL7D5eNPUHnlseEiIsuGQk66RnIE5QWXYDLDj2Lq74,7645
-bioregistry/external/bioportal/agroportal.json,sha256=xd8X9Hp2tOA9q40usinuCzzoUa8Zlmb9CNFcrek3uVo,216235
+bioregistry/external/bioportal/agroportal.json,sha256=hZ6lDYi_eVIxKM-KHvgxa3tn0rjRDyz_CDPK9E0kAvE,216764
 bioregistry/external/bioportal/agroportal.py,sha256=Y5KGAkLqSoSS9czW0oFe7CNLzsiByLxtC3LLb5HB3XQ,147
 bioregistry/external/bioportal/bioportal.json,sha256=MSNIlCR4BHCbYIEnvJIl6waeweai7BrLQNUjYMn8gyI,761456
 bioregistry/external/bioportal/bioportal.py,sha256=8YSiaisYPPc3TkxE7GPrZz2s-mRjV6nXAXzmJ5U0NBs,1011
@@ -150,16 +154,16 @@ bioregistry/external/cropoct/processed.json,sha256=EHkMx_ywPXsGtXSz9DK-DWDMXEi4_
 bioregistry/external/edam/__init__.py,sha256=4rkiMRlFjfEcYXKx8TM8KWPV2H58kxr0cavJoK2LrbQ,1715
 bioregistry/external/edam/processed.json,sha256=3jmBdNwwCXtXZw4jf40riBOHC_HE2GAnYIcnStm4N0k,45513
 bioregistry/external/fairsharing/__init__.py,sha256=bk4EfQIA40mU2xkVYq_Ipl4Mnq79qUVBMfekxU4woqE,5364
-bioregistry/external/fairsharing/processed.json,sha256=kIhnNRnfeDoSO3omfpThjcEdVlzalxQWH_wOeW_SkDE,904667
+bioregistry/external/fairsharing/processed.json,sha256=tMA1c-qDzrnBUe0urqKNisI8ohFc9APoC4zZrkpiqzI,910405
 bioregistry/external/go/__init__.py,sha256=ZrVhZfi0uowNWxymNarFm8TeqxFFRE1HzXB-5kBcz98,4104
 bioregistry/external/go/processed.json,sha256=9xHAqVtUgwPmZZP3byxf585MC3UABNMVoZ2ImW8LTnA,146014
 bioregistry/external/go/processing_go.json,sha256=fuubtH1RyiBWFrMnZq9iT83dlN_uFtyX5uZPVlfrwfo,137
 bioregistry/external/hl7/OID_Report.csv,sha256=7Z2mu6gRb-KIEIkniwfcF_KD3ycL6SBfPEBDOxRlJlI,319976
 bioregistry/external/hl7/__init__.py,sha256=YfwcyCp1IzdxsCVVw9Dy77NS3u4q_T0DeyQrTjNB7FQ,2131
 bioregistry/external/integbio/__init__.py,sha256=Bpsf4-rgPixVa-_YW0IGYuLVkQ9xRpY1DVKd_Joiuz8,5268
-bioregistry/external/integbio/processed.json,sha256=CjDlI067QJp7thh95fXHvWcSRdSD6xLbgwNgexkt5wQ,1796147
+bioregistry/external/integbio/processed.json,sha256=rzejF6evYRWHrpNJ7YXhQjdblJ9Qq-WtbbkxMyEidEs,1796188
 bioregistry/external/lov/__init__.py,sha256=18vZoxRhvX6UqQLAHmyHEMrIB_8Xe4KSGXSNd_PdCw0,2655
-bioregistry/external/lov/processed.json,sha256=e7LWe7xhaiBOMz9lCdAbsYAVWotheNmB5NPhaspJRC8,479432
+bioregistry/external/lov/processed.json,sha256=AmorG5N4kEMlrBf4QklEu5MNWHGeaPX8xoRLVJCyxEY,480851
 bioregistry/external/miriam/.DS_Store,sha256=UgtGnk8l1Yy0lhP02coFpdu_O1ethJwPURlpZRTp0LY,6148
 bioregistry/external/miriam/__init__.py,sha256=SJMcH2Nh00tT0uCfl4yYCgsi3XC1OD6w1JnAZnEzzJ0,4768
 bioregistry/external/miriam/processed.json,sha256=0IUtSsNECP-4GVbz6Ol3QIFUbsn-m-fZWvjqnV2P10M,596526
@@ -168,9 +172,9 @@ bioregistry/external/n2t/processed.json,sha256=2SRCY0OnRTjoSV1t6by5xEaqD_wDVK3xG
 bioregistry/external/ncbi/__init__.py,sha256=276xtZL1b2s9vS8voXuaNybQX6sEtoKyViK4WAfuDb8,5573
 bioregistry/external/ncbi/processed.json,sha256=2bnV32V-vMJmpQDMTEQkdhG28A3Vvfs_67mI2ZPqePY,18072
 bioregistry/external/obofoundry/__init__.py,sha256=XWZpAfCCJCtOxFUvA3xRxgMaFLerHQZoUzByq-AQ1mg,5351
-bioregistry/external/obofoundry/processed.json,sha256=_TOdQscMff6v2tuoo9PstHUsCLVfW7VxBHdP0EBq9S0,225532
+bioregistry/external/obofoundry/processed.json,sha256=bbVOafzCQaMVj6fpJvE8COOpdywB7rgEhp1OLnSfc40,225668
 bioregistry/external/ols/__init__.py,sha256=EpX_3gpB6Lc5PpqXF_tvAmr57fAVbBtQqswDlrfTC7w,11541
-bioregistry/external/ols/processed.json,sha256=tKB9IeBmRBYcT0cqsPq7DMxsrCsumyHN4VQnSVHbseA,161219
+bioregistry/external/ols/processed.json,sha256=GkjV0y-6nzWgOO_0heDGtEjhX8JehDHxXoo5SP4Vs5c,163289
 bioregistry/external/ols/processing_ols.json,sha256=nxKL7Mi12vmo7v2LWSx_Ryd8U2bPuebN1kBW1FYHSPs,35976
 bioregistry/external/ols/tib-processed.json,sha256=LQvtTlcAavxLirqkylBkhlcTsG9JtXBbB4eNQ7KoKtI,198055
 bioregistry/external/ols/tib-processing-config.json,sha256=qQsdTmQTnM-ZCLj-rmztJV25lrJqQcg9esQbYGVB1f4,29
@@ -181,7 +185,7 @@ bioregistry/external/pathguide/__init__.py,sha256=Q6p01FuBU-PxSJUFrZP-fqE_ZOV_lM
 bioregistry/external/prefixcommons/__init__.py,sha256=Nka5nbxg0Nh5YSbvYut2p6GtxXXA5dnMt_HPRlnXgCA,9154
 bioregistry/external/prefixcommons/processed.json,sha256=RlHKDfPca_f38FOwx7UTU_HUlP4Zuq6_jvLuTbx9wh0,514876
 bioregistry/external/re3data/__init__.py,sha256=XyKol_Hhej4kbc56d6COc6MjoUBVrThrOeMurzciRwM,6578
-bioregistry/external/re3data/processed.json,sha256=3RMG5Z7icoLfiRVnetLcGd5xyiZRbPG8Oy8qiThWugI,2718882
+bioregistry/external/re3data/processed.json,sha256=tS5jdc-uEoWExGj2lEWIEksqaMT1Xo_tyYl9ZD2tJeM,2719804
 bioregistry/external/rrid/__init__.py,sha256=NEKpP5N2xPt5K4hw8fsDEbOmwfh8yLoHC4Yl50iSbVQ,3780
 bioregistry/external/togoid/__init__.py,sha256=AUZn69q0Di7o5yb11kGyi8QF9RIFkgiAvZkgnjkmfHo,3506
 bioregistry/external/togoid/processed.json,sha256=h2LeypcVdJvL6wByOo8lJeLCFr4_UQb1EfVR6FjJXEg,81494
@@ -210,23 +214,23 @@ bioregistry/record_accumulator.py,sha256=gbRPS7eWf3daZyuEVCxC-zUqDPz7eX0noqJpoAy
 bioregistry/reference.py,sha256=7r13osgKqjeTzHu84MPuNRbxWYmZ89eBgdaPHHxpL2o,9020
 bioregistry/resolve.py,sha256=j1Z65pN2NvNsPX5ywhbio_kefUoqTT6MSsnoa-H7nWI,31953
 bioregistry/resolve_identifier.py,sha256=YsMIcog9uXQt6IirqJ34yKmv-3kY97yNoi-IK3Ft7tw,17000
-bioregistry/resource_manager.py,sha256=fK4NU3-3q4gnm6tDLBsZmaqlIPSzBUB209k68NX0E3Y,82581
+bioregistry/resource_manager.py,sha256=BN9E1X_m76iB2avt6T-7XJ4UB6pIcG2aUsvkJuznmSQ,82737
 bioregistry/schema/.DS_Store,sha256=ZtEuRder-nSDznMn7EklKQngSW-_kJxHtcU0KF_qRbc,6148
 bioregistry/schema/__init__.py,sha256=P_YbooDhrvtLt1L-6DrGbB0y2vsk_FxUXCbUIQNCZEo,957
 bioregistry/schema/constants.py,sha256=R_UgSWWjlm1T9DdbG3VQXt1Pq4HNucHPV5sXJNQSlso,13619
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